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Onto-Tools specifications

Information


Unique identifier OMICS_26182
Name Onto-Tools
Alternative name ROnto Tools
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No

Documentation


Maintainers


This tool is not maintained anymore.

Additional information


https://bioconductor.org/packages/release/bioc/vignettes/ROntoTools/inst/doc/rontotools.pdf

Information


Unique identifier OMICS_26182
Name Onto-Tools
Alternative name ROnto Tools
Software type Package/Module, Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.8.0
Stability Stable
Requirements
methods, BiocGenerics, RUnit, graph, Rgraphviz, KEGGgraph, boot, KEGGREST
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Sorin Draghici
  • person_outline Calin Voichita

Additional information


https://bioconductor.org/packages/release/bioc/vignettes/ROntoTools/inst/doc/rontotools.pdf

Publication for Onto-Tools

Onto-Tools citations

 (31)
library_books

Highly Expressed Integrin α8 Induces Epithelial to Mesenchymal Transition Like Features in Multiple Myeloma with Early Relapse

2016
Mol Cells
PMCID: 5223107
PMID: 28008160
DOI: 10.14348/molcells.2016.0210

[…] d University School of Medicine, USA: http://jtreeview.sourceforge.net) (). To investigate the biologically relevant pathways most impacted by the gene input list, the online program Pathway-Express (Onto-Tools, Wayne State University, Detroit, MI, USA; http://vortex.cs.wayne.edu/Projects.html) was used (). Specific biological pathways were defined using the Kyoto Encyclopedia of Genes and Genomes […]

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Regressive Effect of Myricetin on Hepatic Steatosis in Mice Fed a High Fat Diet

2016
PMCID: 5188454
PMID: 27973423
DOI: 10.3390/nu8120799
call_split See protocol

[…] Stanford University, Stanford, CA, USA) was performed to identify significantly differentially expressed genes (DEGs) between HFD and HM groups. The DEGs were selected and put into Pathway-Express in Onto-Tools []. Pathway-Express searches the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database for each input gene, and the impact analysis was performed in order to build a list of all a […]

call_split

Menopause induced uterine epithelium atrophy results from arachidonic acid/prostaglandin E2 axis inhibition mediated autophagic cell death

2016
Sci Rep
PMCID: 4979008
PMID: 27506466
DOI: 10.1038/srep31408
call_split See protocol

[…] datasets GSE2883. Venn diagram analysis was performed to identify significantly altered genes that are common after ovariectomy and ER stress challenge. Gene ontology (GO) enrichment was conducted by Onto-Tools, which is a suite of tools for data mining based on information from GO. The identified genes involved in ER stress-induced autophagy in cells deficient in estrogen were clustered using Clu […]

call_split

GFRA3 promoter methylation may be associated with decreased postoperative survival in gastric cancer

2016
BMC Cancer
PMCID: 4794813
PMID: 26984265
DOI: 10.1186/s12885-016-2247-8
call_split See protocol

[…] hical clustering was performed using utilizing the J-express software package [].The filtered dataset, consisting of the 200 most significant ∆β values, was imported into Pathway Express, part of the Onto-Tools software suite [, ], for KEGG (Kyoto Encyclopedia of Genes and Genomes) cellular signaling pathway analysis []. Pathway Express calculates an Impact Factor (IF), which is used to rank the a […]

library_books

Environmentally induced epigenetic transgenerational inheritance of altered SRY genomic binding during gonadal sex determination

2015
PMCID: 4862609
PMID: 27175298
DOI: 10.1093/eep/dvv004

[…] ions with pathways were analyzed for KEGG (Kyoto Encyclopedia for Genes and Genome, Kyoto University, Japan) pathway enrichment using Pathway-Express, a web-based tool freely available as part of the Onto-Tools (http://vortex.cs.wayne.edu). A program based on literature analysis Pathway Studio (Ariadne, Genomics Inc., Rockville, MD) was used to evaluate cellular processes connected to binding targ […]

library_books

Gene bionetworks involved in the epigenetic transgenerational inheritance of altered mate preference: environmental epigenetics and evolutionary biology

2014
BMC Genomics
PMCID: 4073506
PMID: 24885959
DOI: 10.1186/1471-2164-15-377

[…] networks analysis were analyzed for KEGG (Kyoto Encyclopedia for Genes and Genome, Kyoto University, Japan) pathway enrichment using Pathway-Express, a web-based tool freely available as part of the Onto-Tools (http://vortex.cs.wayne.edu) [] as well as KEGG website ‘Search Pathway’ tool (http://www.genome.jp/kegg/tool/search_pathway.html). Global literature analysis of various gene lists was perf […]

Citations

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Onto-Tools institution(s)
Department of Computer Science, Wayne State University, MI, USA; Department of Obstetrics and Gynecology, Karmanos Cancer Institute, Detroit, MI, USA; Department of Molecular Biology and Genetics, Karmanos Cancer Institute, Detroit, MI, USA
Onto-Tools funding source(s)
Supported by the NSF grant number NSF0234806, USMRMC grant number DAMD17-03-2-0035, NIH grant numbers RO1-NS045207-01 and R21-EB000990-01, and Michigan Life Sciences Corridor grant number MLSC-27.

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